Accurately predicting cellular responses to drugs remains a challenge with the potential to reduce experimental screening costs and accelerate drug discovery. Current computational approaches represent compounds through chemical structures, which carry little information regarding their activity within biological syste...
Léa Kaufmann, Lola Le Breton, E. Carraz-Billat et al.· bioRxiv· 0 citations
Residue Embedding Diversity (RED), a metric for protein quality assessment orders of magnitude cheaper than likelihood, and a calibration task that measures model alignment with natural evolutionary distributions are introduced.
Lola Le Breton, David Heurtel-Depeiges, Douglas C. Millar et al.· bioRxiv· 1 citation
Motivation Antimicrobial resistance (AMR) has been identified as a top global public health threat. Accurate AMR phenotype prediction from whole-genome sequencing data is an essential tool for accelerating clinical decision-making and mitigating resistance spread. Although many previous works have explored the use of t...
Alex Aselstyne, E. Karthik, Meriem El Azami et al.· bioRxiv· 0 citations
A high-resolution layer-by-layer interpretability analysis of 8 models from the ESM2 and AMPLIFY families on 22 concepts from human proteome annotations found that these models encode concepts of increasing levels of complexity along their depth: basic physicochemical properties and linear motifs are best captured by e...
Shawn T. Whitfield, Tom Marty, Robert M. Vernon et al.· bioRxiv· 0 citations
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